title: Cancer_cell_in_vivo_C

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

institute: The Francis Crick Institute

data_processing:
Data processing was performed using nf-core/rnaseq pipeline v 3.0
read alingment and gene level quatification was performed using the "--aligner star_rsem" flag in the pipeline above
Differential expression analysis was done with DESeq2.
Assembly: GRCm38, Ensembl release 95
Supplementary files format and content: tab separated estimated counts and TPM for each gene and sample

growth_protocol: 4T1 cells in vitro were grown in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol: RNA was extracted using RLT buffer and RNeasy Micro Kit.

treatment_protocol: Cells were lysed for RNA extraction using RLT buffer and RNA was extracted using RNeasy Micro Kit. RNA quality was measured using a 2100 Bioanalyzer (Agilent). Libraries were prepared using the KAPA Hyper Prep Kit (Roche) and sequenced (sequencing read length, 75 base pairs) in an Illumina HiSeq 4000 system (30 million reads/sample).


title: Cancer_cell_in_vivo_B

status: Public on May 02 2024

type: SRA

city: London

country: United Kingdom

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line


title: BRE_ZT8_4

city: Barcelona

first: Thomas

last: Mortimer

address: Carrer Baldiri Reixac 10-12

country: Spain

institute: IRB Barcelona

description:
JTK_BrainRE.RNAseq_LD.txt
BIOCYCLE_BrainRE_LD.tsv

data_processing:
Quality control and adapter trimming was performed using Trimmomatic (version 0.36).
Reads were aligned to the mm10 genome (UCSC) using the HISAT2 aligner (version 2.2.1), and subsequently sorted using SAMtools (version 1.3.1). After alignment, read quantification was performed using featureCounts (version 1.6.0) and the resulting count data was then normalized to generate RPKM values using the edgeR ‘rpkm’ function (version 3.18.1).
Genes exhibiting daily rhythms in expression were identified using the Jonckheere-Terpstra-Kendall (JTK_CYCLE) and BIOCYCLE algorithms. RPKM normalised gene expression values (Log2 transformed) were provided as input. A differential rhythmicity analysis was performed between all four samples using the algorithm DryR.
Genome_build: mm10
Supplementary_files_format_and_content: Text files (.txt) contain the output from the JTK_CYCLE and BIOCYCLE algorithm when applied to the diurnal RNA-seq data sets generated for each clock reconstitution condition. Files contain the rhythmic parameters calculated by the algorithm for each gene detected by RNA-seq. The dryR results file contains the raw output from the algorithm DryR when it is run to compare the rhythmicity of all four clock reconstitution conditions characterised.

molecule: polyA RNA

source_name: Skin epidermis

growth_protocol: Mice were kept in rooms at 22°C degrees with ad libitum access to a standard chow diet, under a 12h:12h light/dark cycle.

extract_protocol:
Mice were sacrificed at the relevant time by C02 asphyxiation, and their backskin was subsequently removed and stored in ice-cold PBS. The hypodermis was then removed from the skin by vigorous scraping using a scalpel. In a petri dish, the skin was floated on 10ml of 1mg/ml dispase (Sigma Aldrich) (in PBS) for 45 minutes at 37°C to enzymatically separate the epidermis. Using a scalpel, the epidermis was separated from the surface of the skin, and then mechanically disaggregated using surgical scissors. The disaggregated epidermis was placed into 10ml of ice cold PBS + 10% chelated FBS to inactivate dispase, and then sequentially filtered through 100µM and 40µM filters, giving a purified extract of epidermal cells. To extract total RNA, one million epidermal cells were lysed in 500µL TRIzol (Invitrogen), vortexed with 100µL chloroform, and then the resulting aqueous layer containing RNA was isolated. The aqueous layer was mixed with 825µL RLT buffer (Qiagen) and 625µL 100% ethanol to induce RNA precipitation. The sample was further processed using an RNeasy mini kit (Qiagen) in accordance with the manufacturers protocol, and RNA was eluted in molecular biology grade water.
Prior to library preparation, RNA integrity was estimated using an RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent). Libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 1x51bp+17bp+8bp using, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

treatment_protocol: To profile daily transcriptional rhythms, for each genotype, the skin of four eight-week-old mice (all males) was collected at six time points throughout the day. Each time point was separated by four hours, with the first sample collected at lights on (ZT0/8:00am).

tag: strain

tag: replicate

tag: time point

tag: gender

value: Male

tag: genotype

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt

tag: clock reconsitution status

value: Brain Reconsituted (BRE)


title: 57_CRO-MA-057

city: Saint Genes Champanelle

first: Daniel

last: Bechet

address: Theix

department: UNH

country: France

institute: INRA

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the human genome (UCSC GRCh38/hg38) with a set of gene model annotations (genes.gtf downloaded from UCSC on October 27 2019 ; GeneIDs come from the NCBI: gene2refseq.gz).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene (Symbol|NCBI GeneID) and every sample

organism: Homo sapiens

source_name: vastus lateralis muscle

extract_protocol:
Total RNA was isolated using a TissueRuptor and RNeasy Fibrous Tissue Mini Kit (QIAGEN) with an on-column DNase digestion (RNase-Free DNase Set, QIAGEN) to avoid genomic DNA contamination. Integrity of RNA samples was verified using an Agilent Bioanalyser with the RNA 6000 Nano labchip® kit (Agilent). Concentration and purity were determined with a Nanodrop ND-1000 spectrophotometer.
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions and sequenced on two lanes on an Illumina NovaSeq 6000 (single-end, 100bp, flow cell S2).

tag: group

tag: Sex

value: male

tag: age (years)

tag: appendicular lean mass (alm)

value: gain

tag: alm variation (%/year)


title: E34_SVZ_SG replicate 2

city: Belfast

first: Aditi

last: Singh

state: Please Select State

address: 97 Lisburn Road, Belfast

department: The Wellcome-Wolfson Institute for Experimental Medicine, SMDBS

institute: Queen's University Belfast

description:
ChIP-seq (paired end)
E34_SVZ_SG_R3
VT1219_S23

library_source: genomic

data_processing:
The RNA-sequencing output was in FASTQ format. After a quality check using FASTQC, the output was aligned to the Ferret genome MusPutFur1.0 (GCA_000215625.1) with Ensembl’s annotations using TopHat2.1.1. Only uniquely mapped reads were retained for further analysis. SAMTOOLS v0.1.19 (Li et al, 2009) was used to convert the BAM output to SAM format and to sort the BAM file. The read counts per gene were calculated using the HTSeq program, (Anders et al, 2015). The DESeq2 package was used to generate normalized read counts and for differential gene expression analysis.
ChIP-sequencing files in fastq format were subjected to quality control using FASTQC. Bowtie2 was used with local parameter for soft clipping of reads and align the reads to Ferret genome MusPutFur1.0 (GCA_000215625.1).   Aligned sam files were sorted, indexed, and converted to the bam format using SAMTOOLS v0.1.19. Peak calling was performed using MACS2 and taking Input as a control. Peaks were merged from all samples as well as replicates to retain all the regions of interest for differential occupancy. qCount from QuasR was used to count reads from all samples in the merged peak regions.
Genome_build: MusPutFur1.0 (GCA_000215625.1)
Supplementary_files_format_and_content: 1. Normalised read Counts for all RNA-seq samples; 2. Read counts in merged peaks regions for ChIP-seq

molecule: genomic DNA

organism: Mustela putorius furo

source_name: Ferret brain (microdissected regions of ferret cortex) Embryonic day 34

growth_protocol: Ferret embryos were obtained by cesarean section of timed?pregnant females upon deep anesthesia with sodium pentobarbital and then perfused transcardially with 4% paraformaldehyde (PFA); postnatal ferrets were deeply anesthetized with sodium pentobarbital prior to transcardiac perfusion with PFA. After perfusion, the brains were extracted, cryoprotected, frozen, and sectioned.

extract_protocol:
Cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125M glycine, scraped off and rinsed twice with cold 10 ml 1X PBS. Cells were pelleted by centrifugation for 7 min at 4°C at 600g. Pellets were resuspended in 10 mL of Buffer L1 (50mM Hepes KOH, pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton-X 100) and incubated at 4°C for 10 min. This was followed by centrifugation for 5 min at 4°C at 1300g. The pellet was again resuspended in 10 ml of Buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) and incubated at room temperature for 10 min, followed by centrifugation for 5 min at 4°C at 1300g. The pellet was then resuspended in 900 µl Buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate, 0.17mM N-Lauroyl sarcosine) containing protease inhibitors and incubated at 4°C for overnight following sonication using Bioruptor plus (Diagenode). After clearing cellular debris by spinning at 14,000 g for 10 min at 4°C DNA 60 µg of chromatin were incubated at 4 °C overnight with respective antibodies after 1h of preclearing. The mixture was then incubated with 40 µl protein A-Sepharose beads preblocked with tRNA and BSA for 3 h at 4°C. Beads were washed twice with 1 ml buffer L3 and once with 1 ml DOC buffer (10 mM Tris (pH 8.0), 0.25 M LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA), and bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. This followed treatment with RNase A (0.2mg/ml) for 30 min at 37°C and then with Proteinase K (50 µg/ml) for 2.5 h at 55°C. The crosslinking was reversed at 65°C overnight with gentle shaking. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and recovered in 40 µl TE buffer.
1. RNAseq libraries were prepared for sequencing using Truseq stranded illumina protocol; 2. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: age/developmental stage

value: Embryonic day 34

tag: treatment

value: Gyrus (SG)

tag: tissue

value: microsdissected SVZ layer


title: 58_VAL-RA-058

value: female

value: stable low


title: BRE_ZT8_3


title: 56_BAR-BE-056

value: stable high


title: E34_SVZ_SG replicate 1

description:
ChIP-seq (paired end)
E34_SVZ_SG_R1
VT1218_S22


title: ctrlCyto4

city: Stockholm

first: Christian

last: Oertlin

address: Tomtebodavägen 23A

country: Sweden

institute: Karolinska Institutet

data_processing:
Read alignment using HISAT default settings
Alignment to reference genome using rpkmForGenes.py (version 11 April 2013)
Genes mapping to multiple places in genome removed
Gene annotation using RefSeq database
Genome_build: hg19
Supplementary_files_format_and_content: Processed data is a .txt file containing rpkms and raw read counts for each sample obtained by the rpkmForGenes.py script

source_name: ATCC MCF7 cells

growth_protocol: MCF7 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 1% L-glutamine (all from Wisent Bio Products).

extract_protocol:
Polysome-profiling
RNAseq libraries were obtained according to the strand specific TruSeq protocol including ribosomal RNA depletion (Ribo Zero)

treatment_protocol: MCF7 cells were serum starved for 12h prior treatment and treated with 4.2nM DMSO or 4.2nM insulin or 4.2nM insulin + 250nM torin1

value: breast adenocarcinoma

tag: morphology

value: Epithelial-like

tag: rna

value: cytosolic

value: DMSO


title: 55_SOU-AN-055

value: sarcopenic


title: Cancer_cell_in_vitro_C

tag: cell line


title: Cancer_cell_in_vivo_A


title: e15wt_gli3_yz052

city: Santa Cruz

first: Bin

last: Chen

state: CA

address: 1156 High St.

department: MCD Biology

country: USA

institute: University of California Santa Cruz

description: e15wt_gli3.idr.optml.narrow.peaks.mm10.bed.trk.gz

data_processing:
Paired end reads were trimmed to 85x85bp and mapped using Bowtie2 against the set of mouse RepeatMasker elements.
Paired end reads that mapped to repeat elements were discarded. The remaining reads were mapped using Bowtie2 to the mm10 genome.
Duplicate mapped reads were removed using samtools.
The repeat-filtered, duplicate-removed control (input DNA) replicate mappings were concatenated into a single set for use in IDR processing.
The repeat-filtered, duplicate-removed mappings were divided into 2 pseudo replicates for each sample for use in IDR processing.
Peaks were called for the replicates and pseudo replicates using MACS2 with a very permissive p-value cutoff of 0.5 to generate a large set of peaks for processing by IDR.
The top 100,000 MACS2 peaks for the replicates and pseudo replicates were processed by IDR and then filtered using  thresholds for the  original replicates, self pseudo replicates, and pooled pseudo replicates of 0.01, 0.02, 0.01 respectively
The optimal set of peaks selected by IDR using the above criteria were extracted into a narrowPeak bed file.
Assembly: mm10
Supplementary files format and content: narrowPeak bed file

source_name: cerebral cortex

extract_protocol:
E15 wild type cortices were dissected, fixed for 10 min with 1% formaldehyde and neutralized with glycine. The cells were lysed, and the chromatin was sheared into 100∼300 bp fragments. Immunoprecipitation reactions were performed using the Gli3 antibody
For ChIP-seq, sequencing libraries were generated from the ChIP-ed DNA and input DNA for control using Ovation Ultralow System V2 kit according to the manufacturer’s protocol.

value: cerebral cortex

tag: developmental stage

tag: antibody

value: wt

value: ChIPseq


title: 54_DOIN-LU-054


title: Pooled Input E34_SVZ_SG

description:
ChIP-seq (paired end)
Input E34_SVZ_SG
VT1217_S21


title: BRE_ZT8_2

tag: strain

tag: replicate

tag: time point

value: Male

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt

value: Brain Reconsituted (BRE)


title: BRE_ZT8_1

tag: gender

tag: genotype

tag: clock reconsitution status


title: BRE_ZT4_4


title: Cancer_cell_in_vitro_B


title: EpCAM_niche_C

source_name: Lung epithelial cells

tag: cell type

value: Lung epithelial cells

value: control


title: Cancer_cell_in_vitro_A


title: BRE_ZT4_2


title: E34_SVZ_LS replicate 1

description:
ChIP-seq (paired end)
E34_SVZ_LS_R1
VT1214_S18

value: Embryonic day 34

value: Sulcus (LS)

value: microsdissected SVZ layer


title: E34_SVZ_LS replicate 2

description:
ChIP-seq (paired end)
E34_SVZ_LS_R4
VT1386_S9


title: E34_SVZ_LS replicate 3

description:
ChIP-seq (paired end)
E34_SVZ_LS_R5
VT1216_S20

value: Gyrus (SG)


title: BRE_ZT4_3


title: 52_MOS-JO-052

tag: group

tag: Sex

value: male

tag: age (years)

tag: appendicular lean mass (alm)

value: gain


title: E34_SVZ_SG replicate 3

description:
ChIP-seq (paired end)
E34_SVZ_SG_R4
VT1387_S10

tag: age/developmental stage

tag: treatment

tag: tissue


title: 51_AUD-LO-051

value: stable high

tag: alm variation (%/year)


title: EpCAM_niche_A


title: EpCAM_distal_lung_C


title: EpCAM_niche_B


title: 53_DOI-DE-053

value: female


title: BRE_ZT4_1


title: 50_DUL-JE-050

value: sarcopenic


title: EpCAM_distal_lung_B


title: E34_VZ_SG replicate 3

description:
ChIP-seq (paired end)
E34_VZ_SG_R6
VT1389_S12

value: microsdissected VZ layer


title: Pooled Input E34_SVZ_LS

description:
ChIP-seq (paired end)
Input E34_SVZ_LS
VT1213_S17


title: BRE_ZT0_3


title: BRE_ZT0_4


title: 49_RAM-GA-049


title: EpCAM_niche_shSox9_C


title: 48_BAR-YV-048


title: E34_VZ_SG replicate 1

description:
ChIP-seq (paired end)
E34_VZ_SG_R3
VT1211_S15


title: EpCAM_niche_shSox9_B


title: 47_GER-CH-047


title: Pooled Input E34_VZ_SG

description:
ChIP-seq (paired end)
Input E34_VZ_SG
VT1209_S13


title: BRE_ZT0_1


title: EpCAM_niche_shSox9_A


title: 46_MUN-MA-046


title: 45_RAM-MA-045

value: lyposynthesis sarcopenic


title: EpiRE_ZT20_4

description:
JTK_EpiRE.RNAseq_LD.txt
BIOCYCLE_EpiRE_LD.tsv

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre wt/wt

value: Epidermis Reconsituted (EpiRE)


title: E34_VZ_LS replicate 3

description:
ChIP-seq (paired end)
E34_VZ_LS_R6
VT1388_S11


title: E34_VZ_LS replicate 2

description:
ChIP-seq (paired end)
E34_VZ_LS_R5
VT1208_S12


title: EpiRE_ZT20_3

value: Male


title: E34_VZ_LS replicate 1

description:
ChIP-seq (paired end)
E34_VZ_LS_R4
VT1384_S7


title: EpCAM_distal_lung_R1


title: E34_VZ_SG replicate 2

description:
ChIP-seq (paired end)
E34_VZ_SG_R5
VT1212_S16


title: LSK, ADT- and HTO-derived cDNA

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Antibody-derived oligonucleotide (ADT) library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

data_processing:
Fastq files were processed and Hashtag antibodies were demultiplexed using the 10x genomics CellRanger 7.0.0 multi pipeline and aligned to the mm10 2020-A mouse genome reference. For CITE-seq library preparation, we utilized same dual purposes library for antibody tags and cell hashing; however, Cell Ranger requires separate, non-identical fastq files for antibody-derived tags (ADT) and Cell Multiplexing Oligo (CMO) libraries. To resolve this, we created separate fastqs for CMO by removing the first sequencing reads of the dual purposes library according to recommendation by 10x genomics. Thereafter, CITE-seq data was analysed with multi module of Cell Ranger to process together the sequencing data of gene expression (GEX), ADT and CMO.
Cell-feature count matrix from all samples were then merged and analysed with Seurat (v4.3.0) following the multimodal pipeline (https://satijalab.org/seurat/articles/multimodal_vignette.html)
Assembly: mm10
Supplementary files format and content: 10x Genomics Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Bone Marrow

extract_protocol:
Mice aged ~6 months were subjected to iron chelator (Deferoxamine, 50 mg/kg) or vehicle control (HBSS) daily regimens for consecutive 7 days, repeated every 4 weeks for a total of 13 months. lineage depleted bone marrow cells were stained for 30 min with antibodies for lineage, Sca-1, c-Kit, TotalSeq C cocktail and sample-specific hashing antibodies. Stained cells were then sorted on Moflo Astrios EQ (Beckman Coulter), and approximately 20,000 Lin-Sca1+ckit+ (LSK) cells were acquired per sample.
Single cell CITE-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics, Pleasanton, CA, USA). FACS-sorted LSK cells from bone marrow were stained and pooled in equal amounts prior to chip loading. Libraries were constructed according to manufacturer instructions. Libraries were purified and paired-end sequenced using NovaSeq 6000 S4 Reagent Kit v1.5 with 150 cycles (Illumina, San Diego, CA, USA).

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: library type

value: ADT + HTO

tag: antibodies/tags

value: TotalSeq-C Mouse Universal Cocktail; Anti-CD135/TotalSeq-C0098 ; Anti-CD34/TotalSeq-C0857 ; Anti CD62P/TotalSeq-C0229 ; Anti CD117/TotalSeq-C0012 ; Anti Hashtag1 (Control)/TotalSeq-C0301 ; Anti Hashtag2 (IC)/TotalSeq-C0302


title: EpiRE_ZT20_2

tag: strain


title: Pooled Input E34_VZ_LS

description:
ChIP-seq (paired end)
Input E34_VZ_LS
VT1205_S9

value: Embryonic day 34

value: Sulcus (LS)


title: EpiRE_ZT20_1

tag: replicate


title: 43_SER-LO-043


title: LSK, mRNA-derived cDNA

description: RNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: Wild-type mouse liver #2

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

country: Japan

institute: Tokyo Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads on containing ploy- N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http:// ) directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Assembly: mm10
Supplementary files format and content: GTF

source_name: Liver

extract_protocol:
Total RNA was prepared from liver specimens using miRNeasy RNA isolation kit (Qiagen, Inc.). Eliminate DNA contamination using DNase.
Subsequently, sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB,USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C be fore PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: C57BL/6 background

tag: age

value: WT


title: 42_FLA-RE-042

value: male


title: Wild-type mouse liver #1


title: E30_VZ_SG replicate 3

description:
ChIP-seq (paired end)
E30_VZ_SG_R3
VT1204_S8

source_name: Ferret brain (microdissected regions of ferret cortex) Embryonic day 30

value: Embryonic day 30


title: EpiRE_ZT16_4

tag: time point

tag: gender


title: BRE_ZT0_2

description:
JTK_BrainRE.RNAseq_LD.txt
BIOCYCLE_BrainRE_LD.tsv

tag: genotype

value: Arntl stopFL/stopFL ; K14Cre wt/wt ; Syt10-Cre tg/wt

tag: clock reconsitution status

value: Brain Reconsituted (BRE)


title: E30_VZ_SG replicate 2

description:
ChIP-seq (paired end)
E30_VZ_SG_R2
VT1203_S7

value: Gyrus (SG)

value: microsdissected VZ layer


title: 41_JUL-LO-039

tag: group

value: stable high


title: EpiRE_ZT16_3

value: Male

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre wt/wt

value: Epidermis Reconsituted (EpiRE)


title: DICER1 mutant mouse liver #2

value: DICER1 mutant


title: 40_BAR-MA-038

tag: Sex

value: female

value: gain


title: 39_GEN-HU-041

tag: age (years)


title: DICER1 mutant mouse liver #1


title: 44_DEM-NO-044

tag: appendicular lean mass (alm)

value: sarcopenic


title: mut4

city: Los Angeles

first: Tingwei

last: Guo

address: 2250 Alcazar St

department: CCMB

institute: usc

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
Upper quartile was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: incisor

extract_protocol:
RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
cDNA library preparation and sequencing were performed at the USC Molecular Genomics Core.

treatment_protocol: IP injection of Tamoxifen at the concentration of 0.2mg/g (mouse weight)

value: incisor

value: Tamoxifen injection

tag: time


title: 38_DEC-SE-040


title: EpiRE_ZT16_1


title: E30_VZ_LS replicate 3

description:
ChIP-seq (paired end)
E30_VZ_LS_R3
VT1200_S4

tag: age/developmental stage

tag: treatment


title: Pooled Input E30_VZ_SG

description:
ChIP-seq (paired end)
Input E30_VZ_SG
VT1201_S5

tag: tissue


title: EpiRE_ZT12_3


title: EpiRE_ZT12_4


title: 37_FON-JE-037

tag: alm variation (%/year)


title: 36_FON-LU-036


title: E30_VZ_LS replicate 2

description:
ChIP-seq (paired end)
E30_VZ_LS_R2
VT1199_S3

value: Sulcus (LS)


title: EpiRE_ZT12_2


title: mut2


title: 35_MON-AN-035

value: male


title: ctl2

value: WT


title: E30_VZ_LS replicate 1

description:
ChIP-seq (paired end)
E30_VZ_LS_R1
VT1198_S2

value: Embryonic day 30


title: Pooled Input E30_VZ_LS

description:
ChIP-seq (paired end)
Input E30_VZ_LS
VT1197_S1


title: EpiRE_ZT12_1


title: ctl4


title: EpiRE_ZT8_4


title: E30_VZ_SG replicate 1

description:
ChIP-seq (paired end)
E30_VZ_SG_R1
VT1202_S6


title: 33_BES-AL-033


title: EpiRE_ZT16_2

description:
JTK_EpiRE.RNAseq_LD.txt
BIOCYCLE_EpiRE_LD.tsv


title: ESR1-YAP1_shESR1_Veh

city: Pittsburgh

first: Megan

middle: E.

last: Yates

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

description:
YAP1_gained.csv
YAP1_VolcanoPlot.csv
YAP1_peaks.csv

data_processing:
ChIP-seq reads were aligned to the Hg38 reference genome assembly using Bowtie v2.0.
Peaks were called using MACS v2.0 with the significant cut-off q-value<0.1.
Differential binding sites based on genomic occupancy were identified and gained and lost sites were analyzed between ESR1-WT and each fusion using Diffbind.
Heatmaps were generated using Seqplots and gene annotation in a ± 100kb range of all peaks was performed using Binding and Expression Target Analysis (BETA).
ESR1 motif counts were calculated using FIMO (Find Individual Motif Occurrences) from MEME Suite v5.5.
Assembly: hg38
Supplementary files format and content: CSV files listing peaks gained in comparison to ESR1-WT cells treated with vehicle.

source_name: T47D shESR1

growth_protocol: Cells were grown in RPMI-1640 (#11875-119, Life Technologies) media at 37 °C and 5% CO2 before three days of hormone deprivation (media change to improved MEM (#MT10026CV, Fisher Scientific) supplemented with 10% CSS).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Post-quenching and lysis, chromatin was sonicated for 10 cycles of 30 second pulses.
ChIP-seq libraries were prepared using TruSeq ChIP Library preparation. DNA sequencing was performed on an Illumina NextSeq 2000 P3 flow cell 100 at 2x61bp reads with approximately 80 million reads per sample (overall 1.2 billion reads).

treatment_protocol: Wildtype ER cells were treated with 1nM estradiol (#E8875, Sigma) for 45 minutes. All other cell lines were treated with equal volume 100% ethanol for 45 minutes.

tag: cell line

value: T47D shESR1

tag: cell type

value: No special type breast cancer cell line

value: Veh

tag: duration

tag: chip antibody

value: HA (Cell Signaling Technology #3724S, RRID:AB_1549585)


title: 34_MOH-AN-034

value: stable high


title: ESR1-YAP1_shESR1_Veh_Input


title: 32_MIC-JE-032


title: ESR1-SOX9_shESR1_Veh

description:
SOX9_gained.csv
SOX9_VolcanoPlot.csv
SOX9_peaks.csv


title: Endosperm_crwn1/2_8DAP_mRNA_rep4

city: Cambridge

first: JUNSIK

last: CHOI

state: MA

address: 455 MainSt

institute: WHITEHEAD INSTITUTE

data_processing:
CUT&RUN sequencing data were processed by Epic2 (version 0.0.52), DiffBind (version 3.8.4), DeepTools62 (version 3.4.3) and KaryoploteR63 (version 1.24.0). FASTQ files were trimmed with trim_galore (version 0.6.7) with '--stringency 3', '-r1 32', '-r2 32', '-q 20', '--clip_R1 5', and '--clip_R2 5' options.  Trimmed data were aligned to Arabidopsis genome by Bowtie2 (version 2.3.4.1) with '-L22', '-N 0', and '-X 1000' options. Uniquely mapped reads were extracted by Samtools with 'view -q3' option and Picard MarkDuplicates was used to remove PCR duplicates. Epic2 peak caller64 was used to define H3K27me3 peaks. The reads were passed to Epic2 using H3 reads as control. '--effective-genome-fraction' was set as 1 and bin size was 150. To find DMR between WT and crwn1/2 mutants, DiffBind was used with H3 reads as controls and IgG targets as greylists. Reads were counted using 'dba. count' function with 'summits = TRUE'. DMR genes were defined as genes overlapping any portion of it with DMR. DeepTools bamcompare was used to generate average H3K27me3/H3 ratio on genomic regions in Fig. 5a and Extended Data Fig. 6a,c,e,g with '--operation ratio', '--scaleFactorsMethod readCount', '--skipNonCoveredRegions', and '-bs 20' options.
FASTQ files were trimmed with trim_galore (version 0.6.7) with '-q 25' and '--stringency 3' options. To align trimmed sequences, genome files for STAR (version 2.7.1a) were first generated using STAR 'genomeGenerate' mode and TAIR10 whole genome sequence with '--genomeSAindexNbases 12' and '--sjdbOverhang 30' options. Trimmed sequences were aligned to the genome files using STAR with '--alignSoftClipAtReferenceEnds No', '--alignEndsType EndToEnd', '--outSAMstrandField None', '--runThreadN 1', '--outFilterType BySJout', '--outFilterMultimapNmax 5', '--outFilterMismatchNmax 10', '--outFilterMismatchNoverReadLmax 0.05', '--alignIntronMin 70', '--alignIntronMax 5000', '--alignMatesGapMax 100000', and '--outFilterIntronMotifs RemoveNoncanonical' options. PCR duplicates were removed using Picard MarkDuplicates (version 1.121). These trimmed and de-duplicated reads were indexed by Samtools59 (version 1.11) and counted by htseq-count60 (version 1.99.2) with '--mode=intersection-nonempty' and '--nonunique=all' options. Differential expression analysis was performed using DESeq261 (version 1.36.0) with 'DESeqDataSetFromHTSeqCount' function. We included genes only when the gene has at least 10 counts and at least three samples suffice this condition using 'keep <- rowSums(counts(deseqdataset) >= 10) >= 3'. For leaf RNA-seq, this was changed to 6 counts and 2 samples as there are less replicates than endosperm.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: CUT&RUN peak bed files generated by Epic2
Supplementary files format and content: RNA-seq read count csv files counted by HTSeq-count

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: Endosperm 6C nuclei

extract_protocol:
For endosperm CUT&RUN, seeds from 4 to 7 siliques  were pulverized with a pestle (AXYGEN #PES-15-B-SI) in a 1.5mL tube containing 100μL CyStain UV Precise P Nuclei Extraction Buffer (Sysmex #05-5002-P02). 800μL staining buffer (Sysmex #05-5002-P-01) was added and mixed. The nuclei solution was filtered with two CellTrics 30μm disposable filters (Sysmex #04-004-2326) in tandem. The filtered solution was sent to Whitehead Flow Cytometry Core Facility and sorted by BD FACSAria II using 100 um nozzle, 2500 plates voltage and 20 sheath pressure setups. This process was repeated several times to acquire enough number of 6C nuclei. For leaf CUT&RUN, 2 to 3 of 5th leaves were first chopped with a clean razor blade on a petri dish with 150μL of the nuclei extraction buffer and then 1200 μL of the staining buffer was added after the chopping. The mixture was filtered in the same way as the endosperm. The flow cytometry sorting procedure is the same as the endosperm CUT&RUN. For endosperm mRNA-seq, seeds from 1 to 5 of siliques were used with the same methods as in the endosperm CUT&RUN. The numbers of siliques used and nuclei collected for each sample are available in Supplementary Data 6 in the linked publication.
6C nuclei in seeds were sorted by FANS above and used for CUT&RUN. CUT&RUN procedure and library preparation protocol used in this study is described by Zheng and Gehring 2019. We used IDT for Illumina - TruSeq DNA UD indexes. The library was checked with Agilent BioAnalyzer 2100 at Whitehead Genome Technology Core to ensure no primer dimers are left in the samples. The library was sequenced using NovaSeqSP 6000 and NovaSeq SP v1.5 reagents with 50 bp by 50 bp paired end setup in Whitehead Genome Technology Core.  6C seed nuclei sorted by FANS described above were used for RNA-seq. Library was prepared following the protocols provided by the manufacturer in SMART-Seq mRNA LP kit (Takara Bio #634768) and Unique Dual Index Kit (U001-U024) (Takara Bio #634756) with some modifications. Although the manufacturer recommended cDNA synthesis with up to 1000 cells and no indication of nuclei numbers, we used up to 3000 nuclei, which did not hinder the downstream procedure. The cDNA and library were purified as indicated in the manufacturer's protocol with AMPure XP beads (Beckman Coulter #A63881). After the library amplification and purification, we checked the fragment length using an Agilent BioAnalyzer 2100 at Whitehead Genome Technology Core. If there are leftover primer-dimers or other small fragments detected, additional purification with 1:1 bead to sample volume was performed and re-analyzed by the BioAnalyzer. The purified samples were sequenced by Whitehead Genome Technology Core using NovaSeq 6000 and NovaSeq SP v1.5 reagents. Paired end read lengths were 50 bp by 50 bp.

value: Endosperm 6C nuclei

tag: time point


title: Endosperm_crwn1/2_8DAP_mRNA_rep3


title: ctl1


title: mut3


title: EpiRE_ZT8_2

tag: strain

tag: replicate

tag: gender

value: Male

value: Arntl stopFL/stopFL ; K14Cre tg/wt ; Syt10-Cre wt/wt

value: Epidermis Reconsituted (EpiRE)


title: EpiRE_ZT8_3

tag: genotype

tag: clock reconsitution status


title: ESR1-SOX9_shESR1_Veh_Input


title: Endosperm_crwn1/2_8DAP_mRNA_rep2


title: 30_PIC-LA-030

tag: group

tag: Sex

value: female

tag: age (years)


title: ESR1-LPP_shESR1_Veh

description:
LPP_gained.csv
LPP_VolcanoPlot.csv
LPP_peaks.csv


title: EpiRE_ZT8_1


title: 31_JUL-GE-031

tag: appendicular lean mass (alm)

value: sarcopenic


title: EpiRE_ZT4_4


title: Endosperm_crwn1/2_7DAP_mRNA_rep5


title: ESR1-LPP_shESR1_Veh_Input

tag: treatment


title: 29_REG-RO-029

value: gain


title: Endosperm_crwn1/2_8DAP_mRNA_rep1

tag: tissue


title: EpiRE_ZT4_2


title: ESR1-DAB2_shESR1_Veh

description:
DAB2_gained.csv
DAB2_VolcanoPlot.csv
DAB2_peaks.csv


title: 28_OUL-GI-028

tag: alm variation (%/year)


title: Endosperm_crwn1/2_7DAP_mRNA_rep4


title: 27_POR-AM-027


title: ESR1-∆CTD_shESR1_Veh

description:
Delta_gained.csv
CTD_VolcanoPlot.csv
Delta_peaks.csv

tag: cell line


title: ESR1-DAB2_shESR1_Veh_Input

tag: cell type


title: 26_RIX-MA-026


title: Endosperm_crwn1/2_7DAP_mRNA_rep3


title: EpiRE_ZT4_1


title: Endosperm_crwn1/2_7DAP_mRNA_rep2


title: ESR1-∆CTD_shESR1_Veh_Input

tag: duration


title: EpiRE_ZT0_4


title: ESR1-WT_shESR1_E2

description:
WT_E2_gained.csv
WT_E2_VolcanoPlot.csv
WT_E2_peaks.csv

tag: chip antibody


title: 25_SOU-RO-025


title: 24_CRO-MA-024

value: stable low


title: EpiRE_ZT4_3

tag: time point


title: Endosperm_crwn1/2_6DAP_mRNA_rep2


title: 23_IMB-GA-023


title: ESR1-WT_shESR1_E2_Input


title: EpiRE_ZT0_1

tag: strain


title: Endosperm_crwn1/2_6DAP_mRNA_rep1


title: ESR1-WT_shESR1_Veh

description:
WT_E2_gained.csv
WT_E2_VolcanoPlot.csv
WT_V_peaks.csv


title: 21_BER-LO-021


title: EpiRE_ZT0_2

tag: replicate


title: Sample-2: CX01_RNASeq, biological rep2

city: Richmond

first: chunjun

last: zhan

address: 2131 NAPA St

institute: JEBI

description: Cells were incubate in YPD medium overninght, and then transfer into Delft medium for 16h, finally cells were transfer into Delft medium without glucose but with 1% methanol as sole carbon source. Cells were collected at OD600 around 1.0

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome (http://cenpk.tudelft.nl) using TopHat (v 2.0.12)
Cufflinks version 2.2.166 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D

organism: Saccharomyces cerevisiae

source_name: P. Paox1-SKL, P. Pdas1-skl, P. pDAK, B. mMDH3-skl, B. mACT1-skl, P. pPYC, P. sXR, P. sXDH, P. sXK, PEX5, ∆PEX31, ∆PEX32, S.c MDH2, S. cMDH3, S. Cnde1

growth_protocol: Shake flask 30 ˚C, 200rpm

extract_protocol: Send to GENEWIZ


title: 20_CHI-RO-020


title: ESR1-WT_shESR1_Veh_Input


title: Endosperm_crwn1/2_7DAP_mRNA_rep1


title: Endosperm_WT_7DAP_mRNA_rep4


title: Sample-3: CX01_RNASeq, biological rep3


title: Endosperm_crwn1/2_6DAP_mRNA_rep3


title: Bulk RNA-seq data, patient 3

city: Somerville

first: Daniela

middle: Dolores

last: Russo

state: Massachusetts

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
Raw sequencing data were demultiplexed and aligned to the hg38 genome using publicly available scripts on Terra (github.com/lilab-bcb/cumulus) to produce gene matrices for scRNA, HTO and ADT libraries
For bulk RNA-seq, raw sequencing data were demultiplexed and aligned to the hg38 genome using publicly available scripts on Terra (github.com/broadinstitute/TAG-public)
Cells expressing less than 200 and greater than 2500 genes were excluded from further analysis.
HTO and ADT data were integrated into the final Seurat object utilizing the HTODemux function as part of the Seurat v5 package (Hao et al., 2023)
Assembly: hg38
Supplementary files format and content: R object with patient assignment completed via demultiplexing pipelines

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from purchased buffy coat samples using density gradient media and washed with PBS.
scRNA-seq libraries were generated using an optimized Seq-Well S3 protocol that integrates CITE-Seq (Stoeckius et al., 2017). This involves the loading cells onto specialized arrays, sealing the array with a membrane and performing reverse transcription of single cells. This cells are then reverse transcribed and resulting cDNA is amplified.  Bulk RNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using Maxima RT (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products from scRNA-seq and bulk RNA-seq libraries were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).
CITE-seq library: amplification was performed at 95°C for 5min followed by fourteen cycles at [98°C 20s; 60°C for 45s; 70°C for 1min] and final elongation 72°C for 2min with 5’-CAA GCA GAA GAC GGC ATA CGA GAT [unique 6 nt index] GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT C*C*A-3’ Small RNA RPIxx primer as i7 primer (Illumina).
HASH-seq library: amplification was performed at 95°C for 5min followed by fourteen cycles at [98°C 20s; 60°C for 45s; 70°C for 1min] and final elongation 72°C for 2min wit 5’-CAA GCA GAA GAC GGC ATA CGA GAT [unique 8 nt index] G TGA CTG GAG TTC AGA CGT GTG CTC TTC CGA T*C*T-3’ TruSeq D7xx_Long primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
After bead purification of each of the various libraries, sequencing commenced. Separate sequencing runs were needed for Smart-seq2, and all other libraries. The Smart-seq2 libraries were pooled in equal molarity and loaded onto a NextSeq 2000 P1 kit. scRNA-seq was pooled on 80% of a NextSeq 2000 P3 kit, HTO libraries on 10% of the same run, ADT on the final 10% of the P3 run.

value: Peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: library type

value: mRNA

tag: antibodies/tags


title: EpiRE_ZT0_3

tag: gender

tag: genotype

tag: clock reconsitution status


title: 19_ODD-PA-019

tag: group

tag: Sex

value: male

tag: age (years)


title: Endosperm_WT_7DAP_mRNA_rep3

tag: tissue

value: WT


title: B3: CX01F_RNASeq, biological rep3


title: 18_ZAN-AR-018

tag: appendicular lean mass (alm)

tag: alm variation (%/year)


title: Bulk RNA-seq data, patient 1

tag: cell type


title: B2: CX01F_RNASeq, biological rep2


title: Endosperm_WT_7DAP_mRNA_rep2


title: 22_LAS-MA-022


title: Endosperm_WT_7DAP_mRNA_rep1


title: Sample-1: CX01_RNASeq, biological rep1


title: Endosperm_WT_6DAP_mRNA_rep4


title: 16_LAS-SU-016


title: 17_RIV-AN-017


title: B1: CX01F_RNASeq, biological rep1


title: JUN barcode-variant association

city: Basel

first: Guillaume

last: Diss

address: 66 Maulbeerstrasse

country: Switzerland

institute: FMI

data_processing:
For the barcode-variation association, reads were pre-processed with cutapdapt 1.18 and PEAR0.9.11, additional details in the corresponding manuscript
For the DMS, barcode reads were matched to the expected barcode sequences, aggregated by amino acid substitutions and processed with DimSum
Supplementary files format and content: tab-delimited text file. Contains count and logFC
Library strategy: Amplicon-Seq

molecule: other

organism: Escherichia coli

extract_protocol:
For the barcode variant association, DNA was extracted from the transformed E. coli cells using the NucleoBond® PC 500 kit (Macherey-Nagel, Düren, Germany). For the JUN DMS libraries, DNA was extracted using a custom yeast Midiprep protocol
Sequencing libraries were constructed by PCR with primers cotaining the illumina adapters

tag: cell line


title: Antibody derived tag data, sample 2

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

data_processing:
Raw sequencing data were demultiplexed and aligned to the hg38 genome using publicly available scripts on Terra (github.com/lilab-bcb/cumulus) to produce gene matrices for scRNA, HTO and ADT libraries
For bulk RNA-seq, raw sequencing data were demultiplexed and aligned to the hg38 genome using publicly available scripts on Terra (github.com/broadinstitute/TAG-public)
Cells expressing less than 200 and greater than 2500 genes were excluded from further analysis.
HTO and ADT data were integrated into the final Seurat object utilizing the HTODemux function as part of the Seurat v5 package (Hao et al., 2023)
Assembly: hg38
Supplementary files format and content: R object with patient assignment completed via demultiplexing pipelines
Library strategy: CITE-seq

value: ADT

value: TotalSeq™-A Human Universal Cocktail


title: Antibody derived tag data, sample 1


title: Endosperm_WT_6DAP_mRNA_rep3


title: Endosperm_WT_6DAP_mRNA_rep2


title: 15_OLI-IR-015


title: 14_DIG-JE-014


title: Endosperm_WT_6DAP_mRNA_rep1


title: Bulk RNA-seq data, patient 2


title: liver, NC-3-H3K9me3

city: Wuhan

first: Mingliang Wei

last: Mingliang Wei

state: Hubei

address: 299 Bayi Road, Wuchang District

country: China

institute: Wuhan University

data_processing:
Low-quality bases and adapters were removed by Fastp version 0.23.4.
ChIP-seq reads were aligned to the mm10 genome assembly using with bowtie2-align-s version 2.3.5.1.
H3K27ac peaks were called using macs2 2.1.1 with the following setting -f BAMPE -g mm --nomodel --keep-dup all -B --extsize 147 -p 1E-6 --broad --broad-cutoff 1E-6
H3K9me3 peaks were called using macs2 2.1.1 with the following setting -f BAMPE -g mm --nomodel --keep-dup all -B --extsize 147 -p 1E-4 --broad --broad-cutoff 1E-4
bigWig files were generated using the deeptools 3.0.2 bamCoverage with the following setting -bs 10 --normalizeUsing RPKM
Assembly: mm10
Supplementary files format and content: bigWig

growth_protocol: All mouse were housed in a controlled environment with a 12-hour light/dark cycle and provided food and water ad libitum. The ambient temperature was maintained at 24±2℃, with a relative humidity of 45%(Animal Center of College of Life Sciences, Wuhan University).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).  Libraries were sequenced by Illumina Hi-seq X Ten platform with pair-end reads of 150 bp.

treatment_protocol: C57BL/6 male mouse aged 5 weeks ~ 20g were randomly divided into normal group and MCD group (n=5/group). After one week of adaptive feeding, normal group was fed with maintenance diet and MCD group was fed with methionine and choline deficiency diet (Research Diets, A02082002B) for 6 weeks.

value: Liver

tag: chip antibody

tag: treatment

value: NC


title: liver, NC-3-Input


title: 13_DEL-CL-013

value: stable high


title: liver, NC-3-H3K27ac


title: Leaf_crwn1/2_IgG_rep3

data_processing:
CUT&RUN sequencing data were processed by Epic2 (version 0.0.52), DiffBind (version 3.8.4), DeepTools62 (version 3.4.3) and KaryoploteR63 (version 1.24.0). FASTQ files were trimmed with trim_galore (version 0.6.7) with '--stringency 3', '-r1 32', '-r2 32', '-q 20', '--clip_R1 5', and '--clip_R2 5' options.  Trimmed data were aligned to Arabidopsis genome by Bowtie2 (version 2.3.4.1) with '-L22', '-N 0', and '-X 1000' options. Uniquely mapped reads were extracted by Samtools with 'view -q3' option and Picard MarkDuplicates was used to remove PCR duplicates. Epic2 peak caller64 was used to define H3K27me3 peaks. The reads were passed to Epic2 using H3 reads as control. '--effective-genome-fraction' was set as 1 and bin size was 150. To find DMR between WT and crwn1/2 mutants, DiffBind was used with H3 reads as controls and IgG targets as greylists. Reads were counted using 'dba. count' function with 'summits = TRUE'. DMR genes were defined as genes overlapping any portion of it with DMR. DeepTools bamcompare was used to generate average H3K27me3/H3 ratio on genomic regions in Fig. 5a and Extended Data Fig. 6a,c,e,g with '--operation ratio', '--scaleFactorsMethod readCount', '--skipNonCoveredRegions', and '-bs 20' options.
FASTQ files were trimmed with trim_galore (version 0.6.7) with '-q 25' and '--stringency 3' options. To align trimmed sequences, genome files for STAR (version 2.7.1a) were first generated using STAR 'genomeGenerate' mode and TAIR10 whole genome sequence with '--genomeSAindexNbases 12' and '--sjdbOverhang 30' options. Trimmed sequences were aligned to the genome files using STAR with '--alignSoftClipAtReferenceEnds No', '--alignEndsType EndToEnd', '--outSAMstrandField None', '--runThreadN 1', '--outFilterType BySJout', '--outFilterMultimapNmax 5', '--outFilterMismatchNmax 10', '--outFilterMismatchNoverReadLmax 0.05', '--alignIntronMin 70', '--alignIntronMax 5000', '--alignMatesGapMax 100000', and '--outFilterIntronMotifs RemoveNoncanonical' options. PCR duplicates were removed using Picard MarkDuplicates (version 1.121). These trimmed and de-duplicated reads were indexed by Samtools59 (version 1.11) and counted by htseq-count60 (version 1.99.2) with '--mode=intersection-nonempty' and '--nonunique=all' options. Differential expression analysis was performed using DESeq261 (version 1.36.0) with 'DESeqDataSetFromHTSeqCount' function. We included genes only when the gene has at least 10 counts and at least three samples suffice this condition using 'keep <- rowSums(counts(deseqdataset) >= 10) >= 3'. For leaf RNA-seq, this was changed to 6 counts and 2 samples as there are less replicates than endosperm.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: CUT&RUN peak bed files generated by Epic2
Supplementary files format and content: RNA-seq read count csv files counted by HTSeq-count
Library strategy: CUT&RUN

source_name: Leaf 2,4,8,16C nuclei

value: Leaf 2,4,8,16C nuclei

tag: antibody

value: IgG


title: 12_DEL-JA-012


title: Gene expression, sample 2

description: Seq-Well S3 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell


title: Gene expression, sample 1


title: Leaf_crwn1/2_H3_rep3


title: liver, NC-2-Input


title: liver, NC-2-H3K9me3


title: Leaf_crwn1/2_H3K27me3_rep3


title: Liver macrophages from mice fed CDA-HFD for 10w, bio rep 2

city: Hachioji

first: Kenichi

last: Asano

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Adaptor sequences were removed from raw data using Trimmomatic (ver.0.36.0).
Sequencing reads after trimming were aligned to a mouse reference genome sequence (GRCm38/mm10) in the HISAT2 (ver.2.2.1).
Read counts per gene were calculated using featureCounts (ver.2.0.1) based on GENCODE gene annotation version M25.
The transcripts per million (TPM) normalization was done according to the length of each gene and the sum of mapped reads.
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: fastq

source_name: Liver  macrophages

extract_protocol:
Total RNA from sorted cells was extracted with TRIzol LS reagent and Favorgen RNA Kit (Favorgen)
RNA-seq libraries were prepared using the  Nextera XT Kit (Illumina).

value: Liver  macrophages

value: CDA-HFD 10w


title: Leaf_WT_IgG_rep3


title: 10_PER-JE-007

value: female

value: sarcopenic


title: liver, NC-2-H3K27ac


title: Hashtag oligo data, sample 2

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: HTO


title: Leaf_WT_H3_rep3


title: liver, NC-1-Input


title: Liver macrophages from mice fed CDA-HFD for 10w, bio rep 1


title: 8_SEV-IR-009


title: Liver macrophages from mice fed CDA-HFD for 7w, bio rep 3

value: CDA-HFD 7w


title: 7_VER-LU-008

value: gain


title: liver, NC-1-H3K27ac


title: 6_FRE-RE-004


title: Hashtag oligo data, sample 1

value: Peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)


title: Leaf_crwn1/2_H3_rep2


title: liver, NC-1-H3K9me3


title: Liver macrophages from mice fed CDA-HFD for 10w, bio rep 3

value: WT


title: 5_VER-AG-006


title: Liver macrophages from mice fed CDA-HFD for 7w, bio rep 2


title: liver, MCD-3-Input

value: MCD


title: Liver macrophages from ND-fed mice, bio rep 3

value: Normal diet


title: liver, MCD-3-H3K9me3

value: Liver


title: Liver macrophages from mice fed CDA-HFD for 7w, bio rep 1


title: 11_CAR-PI-11

value: male


title: Leaf_crwn1/2_H3K27me3_rep2


title: 4_DEL-LO-005


title: Liver macrophages from ND-fed mice, bio rep 2


title: 9_ROM-AN-010


title: liver, MCD-3-H3K27ac


title: 3_NOB-JE-001


title: Leaf_WT_H3_rep2


title: Liver macrophages from ND-fed mice, bio rep 1

value: Nomal diet


title: Leaf_WT_H3K27me3_rep3

value: Leaf 2,4,8,16C nuclei


title: 2_MAS-NO-003


title: liver, MCD-2-H3K9me3


title: Leaf_crwn1/2_IgG_rep2

value: IgG


title: liver, MCD-2-Input


title: D30_repeat4

city: Melbourne

first: Hyun Jae

last: Lee

address: 792 Elizabeth Street

department: Department of Microbiology and Immunology

country: Australia

institute: University of Melbourne

data_processing:
Data was aligned using the STAR pipeline.
Assembly: GRCm39
Supplementary files format and content: Tab-separated matrix files and barcode coordinates files
Library strategy: Spatial Transcriptomics (Slide-seqV2)

source_name: Spleen

extract_protocol:
Spleen samples were placed in cryomold immediately after dissection. Fresh frozen tissue was cut into 5μm-thick sections and placed on a 3mm diameter circular array of 10μm diameter mRNA capture beads. Beads were coated in mRNA capture probes consisted of location-specific barcode, a probe-specific UMI, and an mRNA-capturing polyT sequence. Tissue was permeabilised, and mRNAs were captured and ligated to probes.
Sequencing libraries were prepared using the Slide-seqV2 protocol (Stickels et al. 2020 - PMID: 33288904).

value: Spleen

value: All splenic cells

tag: strain

tag: age

value: 6-12 weeks


title: Leaf_WT_H3K27me3_rep2


title: liver, MCD-2-H3K27ac


title: D30_repeat2


title: D30_repeat3


title: Leaf_crwn1/2_IgG_rep1


title: Cux2-Control

data_processing:
For scRNAseq: Raw sequencing reads were demultiplexed with Prase pipeline for sublibrary composition. An indexed reference genome for Ferret genome MusPutFur1.0(GCA_000215625.1) with Ensembl annotations was prepared and used for read alignment and subsequently a feature count matrix was generated using custom Parse pipeline version = 1.1.0. The generated cell-by-gene unique molecular identifier (UMI) count matrix was analyzed using the Seurat R package v.4.3.0. Only cells expressing at least 100 genes with expression in at least 100 cells were kept. UMI counts were then normalized for each cell by the total expression, multiplied by 10,000 and log transformed. Seurat’s default method to identify highly variable genes and scale data for regressing out variation from UMI was used. The scaled data with variable genes were used to perform principal component analysis.
Assembly: MusPutFur1.0(GCA_000215625.1)
Supplementary files format and content: comma separated values files, matrix files, h5ad files
Supplementary files format and content: cell metadata, list of genes, matrix, annotated anndata object in h5ad format

source_name: Brain

extract_protocol:
E37 ferret embryos previously electroporated at E34 were obtained by cesarean section under deep anesthesia with sodium pentobarbital, anesthetized, placed in ice-cold phosphate buffered saline (PBS) (1X) and decapitated. The brains were extracted, the meninges removed in cold Leibovitz’s (1X) L-15 medium with L-Glutamine, without pH indicator (Gibco), and the parietal cortical region was dissected from the electroporated hemispheres under a fluorescence dissecting scope (Leica MZFLIII) using microsurgical knives (MSP) in ice-cold L-15 medium. Microdissected cortical tissue blocks containing GFP+ cells from control or Cux2-OE animals were transferred to 2 ml DNA LoBind tubes (Eppendorf). Tissue pieces were enzymatically dissociated for 35 min at 37ºC using MACS Neural Tissue Dissociation Kit P (Miltenyi Biotec) according to the manufacturer’s instructions. Cells were mechanically suspended using a wide-tipped, fire-polished Pasteur pipette (Fisher Scientific) followed by a P1000 pipette (Gilson). Cell suspensions were filtered to new 2ml DNA LoBind tubes through 40μm PluriStrainer Mini (PluriSelect), pre-wet with Hank’s Balanced Salt Solution (1X) without CaCl2/MgCl2/pH indicator (HBSS, Gibco).  Cells were centrifuged (Spectrafuge 24D, Labnet) 2 times for 5min at 1000rpm, and cell pellets were resuspended in 100 μl of PBS pH7.4 (1X) without CaCl2/MgCl2 (Gibco) containing 0.04% Bovine Serum Albumin (BSA, Sigma-Aldrich). Finally, cell suspensions were re-filtered through 40μm PluriStrainer Mini pre-wet filter. Cell death was estimated using trypan blue 0.4% stain (Thermo Fisher Scientific) using a hemocytometer (BLAUBRAND Neubauer, BRAND) on an inverted microscope (Leica DM IL). Debris-free suspensions with cell viability over 90% were immediately FAC-sorted. Before fixation, cells from control or Cux2 overexpressed embryos were pooled together to meet the minimum specification of 105 starting cells of the protocol. In total, approximately 105 GFP+ cells from control embryos, and 2.5 x 105 GFP+ cells from Cux2-OE embryos, were retrieved. scRNA-seq libraries were generated according to Parse Biosciences protocols: Evercode Cell Fixation v2 and Evercode WT v2. For cell fixation, cell suspensions were centrifuged for 10 min at 200g at 4°C in 15 mL BSA-coated Falcon tubes and resuspended into Cell Prefixation Buffer with BSA 7.5% (Gibco) in 15 mL BSA-coated Falcon tubes. Cell viability was inspected as indicated above before proceeding. No significant cell death or damage was observed. Cell suspensions were incubated in fixation solution followed by addition of permeabilization solution and neutralization buffer, according to the manufacturer’s instructions. Cell suspensions were then centrifuged for 20 min at 200g at 4°C and cell pellets resuspended in 150 µL of nuclear buffer and filtered through a 40μm filter (FALCON). DMSO was added to the cell suspensions for cryopreservation and their cell concentration was estimated with trypan blue 0.4% stain (Thermo Fisher Scientific) using a hemocytometer (BLAUBRAND Neubauer, BRAND) on an inverted microscope (Leica DM IL). Cell suspensions were frozen using a Mr. Frosty Freezing container (Sigma-Aldrich) at -80°C until further use. Libraries were prepared using Parse protocol and sequenced on Novaseq 6000 instrument, and were prepared from n = 3 control or n = 4 Cux2-OE embryos from a single litter.
scRNA-seq libraries were generated according to Parse Biosciences protocols: Evercode Cell Fixation v2 and Evercode WT v2

value: Brain

value: Cortical cells

value: Wild type


title: mut_D10_rep1

city: New York

first: Bogdan

last: Sieriebriennikov

state: NY

address: 100 Washington Sq E

institute: New York University

data_processing:
Mapping and counting was done using STAR v2.6.1d.
Count normalization was done using DESeq2 v1.34.0.
Assembly: Hsal_v8.6
Supplementary files format and content: tab-delimited text files that contain raw counts for each sample
Supplementary files format and content: comma-delimited text file that contains DESeq2-normalized counts for all samples

organism: Harpegnathos saltator

source_name: antenna

extract_protocol:
Antennae were frozen with liquid nitrogen and ground into a fine dry powder using a pestle. RNA was extracted via a standard protocol using TRIzol Reagent, followed by ethanol precipitation. DNase treatment was performed in-solution, followed by a second round of TRIzol-chloroform and ethanol precipitation to remove the treatment.
We used the NEBNext Ultra II RNA Library Prep Kit for Illumina with an input of 110 ng RNA and 12 PCR cycles.

value: antenna

tag: sequencing batch

tag: time apf


title: liver, MCD-1-Input


title: Leaf_crwn1/2_H3_rep1

tag: genotype


title: D30_repeat1


title: liver, MCD-1-H3K9me3


title: Leaf_crwn1/2_H3K27me3_rep1


title: Leaf_WT_IgG_rep2


title: Leaf_WT_IgG_rep1


title: D28_3

description: 10x Genomics

data_processing:
Data was processed using the “cellranger count” pipeline from Cell Ranger version 3.0.2 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

extract_protocol:
Plasmodium-specific CD4+ T cells (PbTII) cells from the spleen were isolated by flow cytometry into 1% BSA/PBS buffer. Ten recipient mice were pooled at each timepoint for isolating splenic PbTII cells. PbTII cells were then sorted as single-cells using the Chromium 10x Genomics platform. Approximately 8,000 cells were loaded per channel onto a Chromium controller (10x Genomics) for generation of gel bead-in-emulsions using 10x Genomics Single Cell 3' Reagent Kit v3.
Sequencing libraries were prepared using Single Cell 3’ Reagent Kits v3 (10x Genomics).

value: CD4-positive alpha-beta T cell


title: mut_D20_rep1


title: D28_2

description: 10x Genomics


title: liver, MCD-1-H3K27ac


title: VZ_A19_P0 replicate 3

description:
RNA-seq (single end)
VZ_A19_P0_R6

data_processing:
The RNA-sequencing output was in FASTQ format. After a quality check using FASTQC, the output was aligned to the Ferret genome MusPutFur1.0 (GCA_000215625.1) with Ensembl’s annotations using TopHat2.1.1. Only uniquely mapped reads were retained for further analysis. SAMTOOLS v0.1.19 (Li et al, 2009) was used to convert the BAM output to SAM format and to sort the BAM file. The read counts per gene were calculated using the HTSeq program, (Anders et al, 2015). The DESeq2 package was used to generate normalized read counts and for differential gene expression analysis.
ChIP-sequencing files in fastq format were subjected to quality control using FASTQC. Bowtie2 was used with local parameter for soft clipping of reads and align the reads to Ferret genome MusPutFur1.0 (GCA_000215625.1).   Aligned sam files were sorted, indexed, and converted to the bam format using SAMTOOLS v0.1.19. Peak calling was performed using MACS2 and taking Input as a control. Peaks were merged from all samples as well as replicates to retain all the regions of interest for differential occupancy. qCount from QuasR was used to count reads from all samples in the merged peak regions.
Genome_build: MusPutFur1.0 (GCA_000215625.1)
Supplementary_files_format_and_content: 1. Normalised read Counts for all RNA-seq samples; 2. Read counts in merged peaks regions for ChIP-seq

source_name: Ferret brain (microdissected regions of ferret cortex) Postnatal day 0

extract_protocol:
Cells were cross-linked in medium containing 1% formaldehyde for 10 min at room temperature, neutralized with 0.125M glycine, scraped off and rinsed twice with cold 10 ml 1X PBS. Cells were pelleted by centrifugation for 7 min at 4°C at 600g. Pellets were resuspended in 10 mL of Buffer L1 (50mM Hepes KOH, pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 5% NP-40, 0.25% Triton-X 100) and incubated at 4°C for 10 min. This was followed by centrifugation for 5 min at 4°C at 1300g. The pellet was again resuspended in 10 ml of Buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0) and incubated at room temperature for 10 min, followed by centrifugation for 5 min at 4°C at 1300g. The pellet was then resuspended in 900 µl Buffer L3 (1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0, 10mM Tris pH 8.0, 100mM NaCl, 0.1% Na-deoxycholate, 0.17mM N-Lauroyl sarcosine) containing protease inhibitors and incubated at 4°C for overnight following sonication using Bioruptor plus (Diagenode). After clearing cellular debris by spinning at 14,000 g for 10 min at 4°C DNA 60 µg of chromatin were incubated at 4 °C overnight with respective antibodies after 1h of preclearing. The mixture was then incubated with 40 µl protein A-Sepharose beads preblocked with tRNA and BSA for 3 h at 4°C. Beads were washed twice with 1 ml buffer L3 and once with 1 ml DOC buffer (10 mM Tris (pH 8.0), 0.25 M LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA), and bound chromatin was eluted in 1% SDS/0.1 M NaHCO3. This followed treatment with RNase A (0.2mg/ml) for 30 min at 37°C and then with Proteinase K (50 µg/ml) for 2.5 h at 55°C. The crosslinking was reversed at 65°C overnight with gentle shaking. DNA was purified by phenol-chloroform extraction followed by ethanol precipitation and recovered in 40 µl TE buffer.
1. RNAseq libraries were prepared for sequencing using Truseq stranded illumina protocol; 2. ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: age/developmental stage

value: Postnatal day 0

value: Caudal Sulcus (A19)

value: microsdissected VZ layer


title: wt_D10_rep2

value: wt


title: Leaf_WT_H3_rep1

value: WT


title: VZ_A19_P0 replicate 2

description:
RNA-seq (single end)
VZ_A19_P0_R4


title: Leaf_WT_H3K27me3_rep1


title: D28_1

description: 10x Genomics


title: 1_MAS-SU-002

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing and trimming were performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the human genome (UCSC GRCh38/hg38) with a set of gene model annotations (genes.gtf downloaded from UCSC on October 27 2019 ; GeneIDs come from the NCBI: gene2refseq.gz).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene (Symbol|NCBI GeneID) and every sample

source_name: vastus lateralis muscle

extract_protocol:
Total RNA was isolated using a TissueRuptor and RNeasy Fibrous Tissue Mini Kit (QIAGEN) with an on-column DNase digestion (RNase-Free DNase Set, QIAGEN) to avoid genomic DNA contamination. Integrity of RNA samples was verified using an Agilent Bioanalyser with the RNA 6000 Nano labchip® kit (Agilent). Concentration and purity were determined with a Nanodrop ND-1000 spectrophotometer.
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions and sequenced on two lanes on an Illumina NovaSeq 6000 (single-end, 100bp, flow cell S2).

tag: group

value: female

value: stable low


title: wt_D10_rep1


title: Endosperm_crwn1/2_IgG_rep3

value: Endosperm 6C nuclei


title: D28

description: 10x Genomics


title: VZ_A19_P0 replicate 1

description:
RNA-seq (single end)
VZ_A19_P0_R3


title: wt_D15_rep3


title: VZ_A17_P0 replicate 3

description:
RNA-seq (single end)
VZ_A17_P0_R6

value: Caudal Gyrus (A17)


title: SI_Tuft_Chat-pos_4

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

description: Sample column 8_Chat_p in rawcounts.csv

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Assembly: GRCm38
Supplementary files format and content: One .csv file containing raw counts for each gene

source_name: Small Intestine

extract_protocol:
Epithelial cells were isolated from the small intestine by washing once with DTT buffer (15 min) and then twice with EDTA buffer (15 min). The supernatants from the two EDTA washes were pooled and stained for EPCAM(PE-Cy7) and CD45(BV605) using standard flow cytometry staining protocol. Chat-GFP+ and Chat-GFP- tuft cells (CD45- EPCAM+ Il25-RFP+) were sorted directly into SMARTer v4 lysis reagents (Clontech). Cells were lysed and cDNA was synthesized.
After amplification, sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina).
Barcoded libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) for 74 cycles, using TruSeq v3, and SBS kits (Illumina). Target read depths were ~5-10 million raw reads per sample.

value: Small Intestine

value: Epithelium (tuft cell)

tag: cell population

value: Chat-pos


title: wt_D15_rep2


title: Endosperm_crwn1/2_H3K27me3_rep3


title: Endosperm_crwn1/2_H3_rep3


title: SI_Tuft_Chat-pos_2

description: Sample column 6_Chat_p in rawcounts.csv


title: VZ_A17_P0 replicate 1

description:
RNA-seq (single end)
VZ_A17_P0_R3


title: VZ_A17_P0 replicate 2

description:
RNA-seq (single end)
VZ_A17_P0_R4


title: wt_D10_rep3


title: SI_Tuft_Chat-pos_1

description: Sample column 5_Chat_p in rawcounts.csv


title: wt_D20_rep3


title: wt_D15_rep1


title: Endosperm_WT_H3_rep3


title: SVZ_A19_E34 replicate 3

description:
RNA-seq (single end)
SVZ_A19_E34_R3
RNAseq_normalizedCount.csv

source_name: Ferret brain (microdissected regions of ferret cortex) Embryonic day 34

value: Embryonic day 34

value: microsdissected SVZ layer


title: SVZ_A19_E34 replicate 2

description:
RNA-seq (single end)
SVZ_A19_E34_R2
RNAseq_normalizedCount.csv


title: Endosperm_WT_IgG_rep3

value: IgG


title: Endosperm_WT_H3K27me3_rep3


title: Endosperm_crwn1/2_IgG_rep2


title: SVZ_A19_E34 replicate 1

description:
RNA-seq (single end)
SVZ_A19_E34_R1
RNAseq_normalizedCount.csv


title: wt_D20_rep2

value: antenna


title: wt_D25_rep3


title: SI_Tuft_Chat-neg_3

description: Sample column 3_Chat_n in rawcounts.csv

value: Chat-neg


title: SVZ_A17_E34 replicate 3

description:
RNA-seq (single end)
SVZ_A17_E34_R3
RNAseq_normalizedCount.csv


title: Endosperm_crwn1/2_H3_rep2


title: SI_Tuft_Chat-neg_1

description: Sample column 1_Chat_n in rawcounts.csv


title: wt_D25_rep2


title: SI_Tuft_Chat-pos_3

description: Sample column 7_Chat_p in rawcounts.csv


title: Endosperm_crwn1/2_H3K27me3_rep2


title: FOG2_WT_rep3 ncRNA-seq

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description:
Total RNA polyA-depleted
IMNTG14

data_processing:
Reads were aligned to mouse genome version mm10 with STAR using parameter.  Counts were retrieved with HTseq (v.0.6.0) in union mode.
edgeR was used for differential expression testing with default settings
genotype specific bigWigs were generated with deeptools tools multibigwigsummary, normalized by CPM and seperating by strand
Assembly: mm10
Supplementary files format and content: comma delimited file with genomic position , normalized counts, and edgeR results
Supplementary files format and content: CPM bigWig

source_name: Wild type left atria from adult mice

extract_protocol:
Hearts were harvested from DTG and NTG animals reared without doxycycline for one week. The left atria of these mice were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, the aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Column
Total RNA was extracted by TRIzol Reagent (Invitrogen), followed by ribosomal and polyA depletion. After RiboZero purification and oligo-dT depletion, RNA Barcoded Libraries were prepared accord- ing to Illumina’s instructions (2013) accompanying the TruSeQ RNA Sample prep kit v2 (Part# RS-122-2001

value: Left Atria

value: Adult


title: SVZ_A17_E34 replicate 2

city: Belfast

first: Aditi

last: Singh

address: 97 Lisburn Road, Belfast

institute: Queen's University Belfast

description:
RNA-seq (single end)
SVZ_A17_E34_R2
RNAseq_normalizedCount.csv


title: Endosperm_WT_IgG_rep2


title: mut_rep7


title: FOG2_WT_rep2 ncRNA-seq

description:
Total RNA polyA-depleted
IMNTG13


title: SI_Tuft_Chat-neg_4

description: Sample column 4_Chat_n in rawcounts.csv


title: wt_D25_rep1


title: VZ_A19_E34 replicate 3

description:
RNA-seq (single end)
VZ_A19_E34_R3
RNAseq_normalizedCount.csv

value: Caudal Sulcus (A19)

value: microsdissected VZ layer


title: Endosperm_WT_H3_rep2

value: WT


title: FOG2_WT_rep1 ncRNA-seq

description:
Total RNA polyA-depleted
IMNTG12


title: VZ_A19_E34 replicate 2

description:
RNA-seq (single end)
VZ_A19_E34_R2
RNAseq_normalizedCount.csv


title: mut_rep6


title: Endosperm_WT_H3K27me3_rep2


title: wt_D20_rep1

value: wt


title: mut_rep5


title: SI_Tuft_Chat-neg_2

description: Sample column 2_Chat_n in rawcounts.csv


title: FOG2_OE_rep3 ncRNA-seq

description:
Total RNA polyA-depleted
IMDTG9

source_name: FOG2 overexpressed left atria from adult mice

value: FOG2 Overexpression


title: VZ_A17_E34 replicate 3

description:
RNA-seq (single end)
VZ_A17_E34_R3
RNAseq_normalizedCount.csv


title: FOG2_OE_rep2 ncRNA-seq

description:
Total RNA polyA-depleted
IMDTG8


title: mut_rep3


title: mut_rep4


title: Endosperm_crwn1/2_H3_rep1

value: Endosperm 6C nuclei


title: Endosperm_crwn1/2_H3K27me3_rep1


title: FOG2_OE_rep1 ncRNA-seq

description:
Total RNA polyA-depleted
IMDTG10


title: SVZ_A17_E34 replicate 1

description:
RNA-seq (single end)
SVZ_A17_E34_R1
RNAseq_normalizedCount.csv

value: Caudal Gyrus (A17)


title: mut_rep2


title: FOG2_WT_rep3

description:
polyA mRNA-seq
LA_WT5

data_processing:
Reads were aligned to mouse genome version mm10 with STAR using parameter.  Counts were retrieved with HTseq (v.0.6.0) in union mode.
DESeq2 was used for differential expression testing with default settings
Assembly: mm10
Supplementary files format and content: comma delimited file with raw counts

extract_protocol:
Hearts were harvested from DTG and NTG animals reared without doxycycline for one week. The left atria of these mice were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, the aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Column
Libraries were prepared from RNA starting with 1 μg per sample and using the mRNA-seq Sample Prep Kit (Illumina) as per recommended instructions. After Ribozero purification and removing only ribosomal RNA, barcoded libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2 (Part# RS-122-2001)


title: VZ_A17_E34 replicate 1

description:
RNA-seq (single end)
VZ_A17_E34_R1
RNAseq_normalizedCount.csv


title: VZ_A19_E30 replicate 3

description:
RNA-seq (single end)
VZ_A19_E30_R3
RNAseq_normalizedCount.csv

source_name: Ferret brain (microdissected regions of ferret cortex) Embryonic day 30

value: Embryonic day 30


title: FOG2_WT_rep2

description:
polyA mRNA-seq
LA_WT3


title: mut_rep1


title: het_rep3


title: Endosperm_WT_H3_rep1


title: FOG2_WT_rep1

description:
polyA mRNA-seq
LA_WT1


title: FOG2_OE_rep4

description:
polyA mRNA-seq
LA_OE9


title: Endosperm_WT_H3K27me3_rep1


title: VZ_A19_E34 replicate 1

description:
RNA-seq (single end)
VZ_A19_E34_R1
RNAseq_normalizedCount.csv


title: mut_D10_rep3


title: het_rep1


title: het_rep2


title: VZ_A19_E30 replicate 2

description:
RNA-seq (single end)
VZ_A19_E30_R2
RNAseq_normalizedCount.csv


title: VZ_A17_E34 replicate 2

description:
RNA-seq (single end)
VZ_A17_E34_R2
RNAseq_normalizedCount.csv


title: VZ_A19_E30 replicate 1

description:
RNA-seq (single end)
VZ_A19_E30_R1
RNAseq_normalizedCount.csv


title: Endosperm_crwn1/2_IgG_rep1


title: FOG2_OE_rep3

description:
polyA mRNA-seq
LA_OE7


title: VZ_A17_E30 replicate 3

description:
RNA-seq (single end)
VZ_A17_E30_R3
RNAseq_normalizedCount.csv


title: mut_D15_rep1


title: VZ_A17_E30 replicate 2

description:
RNA-seq (single end)
VZ_A17_E30_R2
RNAseq_normalizedCount.csv


title: wt_rep1


title: mut_D10_rep2


title: FOG2_OE_rep1

description:
polyA mRNA-seq
LA_OE11


title: wt_rep2


title: mut_lib_1

description: 10X Genomics, double-indexed, nuclei

data_processing:
Demultiplexing and counting were done using cellranger v7.0.0
Assembly: Hsal_v8.6
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Antennae were frozen and ground with a pestle, then Dounce-homogenized in homogenization buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X-100, 0.5 mM RNAseOUT, 1X Promega protease inhibitor, 0.1 mM DTT), filtered, washed and resuspended in 1xPBS+1%BSA+1mM RNAseOUT, then filtered again
We used 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (single-index version for wt_lib_1 and dual-index version for the remaining libraries) and folllowed manufacturer's instructions.

value: orco mutant

tag: biological replicate


title: VZ_A17_E30 replicate 1

description:
RNA-seq (single end)
VZ_A17_E30_R1
RNAseq_normalizedCount.csv

tag: tissue


title: Endosperm_WT_IgG_rep1


title: kidney cell 3290, Lean, 11 weeks

status: Public on May 01 2024

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

description:
kidney cell 3290
1050s_D4

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts values for each sample

source_name: Kidney

extract_protocol:
For labelling of EC and live cells, the kidney cell suspension was incubated with APC-conjugated anti-CD31 antibody (1:100, 551262, BD Biosciences) and Calcein AM (2 µM, C3099, Thermo Fisher Scientific) for 20 min at RT, then centrifugated as above, supernatant removed, and the cell pellet resuspended in FACS buffer and placed on ice. The SmartSeq2 methodology was used for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: kidney

value: Lean

tag: disease state

value: control

value: 11 weeks


title: kidney cell 3291, Lean, 11 weeks

description:
kidney cell 3291
1050s_D5


title: kidney cell 3293, Lean, 11 weeks

description:
kidney cell 3293
1050s_D7


title: kidney cell 3292, Lean, 11 weeks

description:
kidney cell 3292
1050s_D6


title: kidney cell 3294, Lean, 11 weeks

description:
kidney cell 3294
1050s_D9


title: kidney cell 3295, Lean, 11 weeks

description:
kidney cell 3295
1050s_E1


title: kidney cell 3289, Lean, 11 weeks

description:
kidney cell 3289
1050s_D3


title: kidney cell 3284, Lean, 11 weeks

description:
kidney cell 3284
1050s_D16


title: kidney cell 3285, Lean, 11 weeks

description:
kidney cell 3285
1050s_D17


title: kidney cell 3287, Lean, 11 weeks

description:
kidney cell 3287
1050s_D2


title: FOG2_OE_rep2

description:
polyA mRNA-seq
LA_OE13


title: kidney cell 3286, Lean, 11 weeks

description:
kidney cell 3286
1050s_D19


title: kidney cell 3282, Lean, 11 weeks

description:
kidney cell 3282
1050s_D13


title: kidney cell 3288, Lean, 11 weeks

description:
kidney cell 3288
1050s_D22


title: kidney cell 3281, Lean, 11 weeks

description:
kidney cell 3281
1050s_D12


title: kidney cell 3279, Lean, 11 weeks

description:
kidney cell 3279
1050s_D10


title: kidney cell 3276, Lean, 11 weeks

description:
kidney cell 3276
1050s_C8


title: kidney cell 3275, Lean, 11 weeks

description:
kidney cell 3275
1050s_C7


title: kidney cell 3278, Lean, 11 weeks

description:
kidney cell 3278
1050s_D1


title: kidney cell 3272, Lean, 11 weeks

description:
kidney cell 3272
1050s_C3


title: kidney cell 3271, Lean, 11 weeks

description:
kidney cell 3271
1050s_C23


title: kidney cell 3280, Lean, 11 weeks

description:
kidney cell 3280
1050s_D11


title: kidney cell 3277, Lean, 11 weeks

description:
kidney cell 3277
1050s_C9


title: kidney cell 3270, Lean, 11 weeks

description:
kidney cell 3270
1050s_C21


title: kidney cell 3273, Lean, 11 weeks

description:
kidney cell 3273
1050s_C5


title: kidney cell 3274, Lean, 11 weeks

description:
kidney cell 3274
1050s_C6


title: kidney cell 3269, Lean, 11 weeks

description:
kidney cell 3269
1050s_C20


title: kidney cell 3267, Lean, 11 weeks

description:
kidney cell 3267
1050s_C19


title: kidney cell 3268, Lean, 11 weeks

description:
kidney cell 3268
1050s_C2


title: kidney cell 3266, Lean, 11 weeks

description:
kidney cell 3266
1050s_C18


title: kidney cell 3283, Lean, 11 weeks

description:
kidney cell 3283
1050s_D15


title: kidney cell 3262, Lean, 11 weeks

description:
kidney cell 3262
1050s_C13


title: kidney cell 3260, Lean, 11 weeks

description:
kidney cell 3260
1050s_C11


title: kidney cell 3263, Lean, 11 weeks

description:
kidney cell 3263
1050s_C15


title: kidney cell 3256, Lean, 11 weeks

description:
kidney cell 3256
1050s_B8


title: kidney cell 3254, Lean, 11 weeks

description:
kidney cell 3254
1050s_B5


title: kidney cell 3259, Lean, 11 weeks

description:
kidney cell 3259
1050s_C10


title: kidney cell 3257, Lean, 11 weeks

description:
kidney cell 3257
1050s_B9


title: kidney cell 3258, Lean, 11 weeks

description:
kidney cell 3258
1050s_C1


title: kidney cell 3261, Lean, 11 weeks

description:
kidney cell 3261
1050s_C12


title: kidney cell 3249, Lean, 11 weeks

description:
kidney cell 3249
1050s_B19


title: kidney cell 3264, Lean, 11 weeks

description:
kidney cell 3264
1050s_C16


title: kidney cell 3245, Lean, 11 weeks

description:
kidney cell 3245
1050s_B12


title: kidney cell 3252, Lean, 11 weeks

description:
kidney cell 3252
1050s_B22


title: kidney cell 3253, Lean, 11 weeks

description:
kidney cell 3253
1050s_B24


title: kidney cell 3247, Lean, 11 weeks

description:
kidney cell 3247
1050s_B17


title: kidney cell 3244, Lean, 11 weeks

description:
kidney cell 3244
1050s_B11


title: kidney cell 3246, Lean, 11 weeks

description:
kidney cell 3246
1050s_B15


title: kidney cell 3251, Lean, 11 weeks

description:
kidney cell 3251
1050s_B20


title: kidney cell 3248, Lean, 11 weeks

description:
kidney cell 3248
1050s_B18


title: kidney cell 3243, Lean, 11 weeks

description:
kidney cell 3243
1050s_B1


title: kidney cell 3255, Lean, 11 weeks

description:
kidney cell 3255
1050s_B6


title: kidney cell 3242, Lean, 11 weeks

description:
kidney cell 3242
1050s_A9


title: kidney cell 3241, Lean, 11 weeks

description:
kidney cell 3241
1050s_A8


title: kidney cell 3240, Lean, 11 weeks

description:
kidney cell 3240
1050s_A7


title: kidney cell 3265, Lean, 11 weeks

description:
kidney cell 3265
1050s_C17


title: kidney cell 3239, Lean, 11 weeks

description:
kidney cell 3239
1050s_A6


title: kidney cell 3238, Lean, 11 weeks

description:
kidney cell 3238
1050s_A5


title: kidney cell 3237, Lean, 11 weeks

description:
kidney cell 3237
1050s_A4


title: kidney cell 3235, Lean, 11 weeks

description:
kidney cell 3235
1050s_A24


title: kidney cell 3236, Lean, 11 weeks

description:
kidney cell 3236
1050s_A3


title: kidney cell 3234, Lean, 11 weeks

description:
kidney cell 3234
1050s_A23


title: kidney cell 3250, Lean, 11 weeks

description:
kidney cell 3250
1050s_B2


title: kidney cell 3230, Lean, 11 weeks

description:
kidney cell 3230
1050s_A19


title: kidney cell 3232, Lean, 11 weeks

description:
kidney cell 3232
1050s_A20


title: kidney cell 3231, Lean, 11 weeks

description:
kidney cell 3231
1050s_A2


title: kidney cell 3227, Lean, 11 weeks

description:
kidney cell 3227
1050s_A16


title: kidney cell 3228, Lean, 11 weeks

description:
kidney cell 3228
1050s_A17


title: kidney cell 3229, Lean, 11 weeks

description:
kidney cell 3229
1050s_A18


title: kidney cell 3226, Lean, 11 weeks

description:
kidney cell 3226
1050s_A15


title: kidney cell 3225, Lean, 11 weeks

description:
kidney cell 3225
1050s_A12


title: kidney cell 3222, Obese, 6 weeks

description:
kidney cell 3222
067s_P9

value: Obese

value: diabetic nephropathy

value: 6 weeks


title: kidney cell 3224, Lean, 11 weeks

description:
kidney cell 3224
1050s_A11


title: kidney cell 3219, Obese, 6 weeks

description:
kidney cell 3219
067s_P6


title: kidney cell 3216, Obese, 6 weeks

description:
kidney cell 3216
067s_P3


title: kidney cell 3220, Obese, 6 weeks

description:
kidney cell 3220
067s_P7


title: kidney cell 3217, Obese, 6 weeks

description:
kidney cell 3217
067s_P4


title: kidney cell 3214, Obese, 6 weeks

description:
kidney cell 3214
067s_P23


title: kidney cell 3213, Obese, 6 weeks

description:
kidney cell 3213
067s_P22


title: kidney cell 3223, Lean, 11 weeks

description:
kidney cell 3223
1050s_A10


title: kidney cell 3212, Obese, 6 weeks

description:
kidney cell 3212
067s_P21


title: kidney cell 3211, Obese, 6 weeks

description:
kidney cell 3211
067s_P20


title: kidney cell 3209, Obese, 6 weeks

description:
kidney cell 3209
067s_P19


title: kidney cell 3210, Obese, 6 weeks

description:
kidney cell 3210
067s_P2


title: kidney cell 3218, Obese, 6 weeks

description:
kidney cell 3218
067s_P5


title: kidney cell 3206, Obese, 6 weeks

description:
kidney cell 3206
067s_P15


title: kidney cell 3207, Obese, 6 weeks

description:
kidney cell 3207
067s_P16


title: kidney cell 3233, Lean, 11 weeks

description:
kidney cell 3233
1050s_A22


title: kidney cell 3205, Obese, 6 weeks

description:
kidney cell 3205
067s_P14


title: kidney cell 3208, Obese, 6 weeks

description:
kidney cell 3208
067s_P18


title: kidney cell 3204, Obese, 6 weeks

description:
kidney cell 3204
067s_P12


title: kidney cell 3202, Obese, 6 weeks

description:
kidney cell 3202
067s_P10


title: kidney cell 3203, Obese, 6 weeks

description:
kidney cell 3203
067s_P11


title: kidney cell 3201, Obese, 6 weeks

description:
kidney cell 3201
067s_P1


title: kidney cell 3199, Obese, 6 weeks

description:
kidney cell 3199
067s_O8


title: kidney cell 3196, Obese, 6 weeks

description:
kidney cell 3196
067s_O5


title: kidney cell 3198, Obese, 6 weeks

description:
kidney cell 3198
067s_O7


title: kidney cell 3197, Obese, 6 weeks

description:
kidney cell 3197
067s_O6


title: kidney cell 3221, Obese, 6 weeks

description:
kidney cell 3221
067s_P8


title: kidney cell 3215, Obese, 6 weeks

description:
kidney cell 3215
067s_P24


title: kidney cell 3195, Obese, 6 weeks

description:
kidney cell 3195
067s_O3


title: kidney cell 3193, Obese, 6 weeks

description:
kidney cell 3193
067s_O22


title: kidney cell 3190, Obese, 6 weeks

description:
kidney cell 3190
067s_O2


title: kidney cell 3194, Obese, 6 weeks

description:
kidney cell 3194
067s_O23


title: kidney cell 3192, Obese, 6 weeks

description:
kidney cell 3192
067s_O21


title: kidney cell 3186, Obese, 6 weeks

description:
kidney cell 3186
067s_O16


title: kidney cell 3185, Obese, 6 weeks

description:
kidney cell 3185
067s_O13


title: kidney cell 3191, Obese, 6 weeks

description:
kidney cell 3191
067s_O20


title: kidney cell 3184, Obese, 6 weeks

description:
kidney cell 3184
067s_O12


title: kidney cell 3189, Obese, 6 weeks

description:
kidney cell 3189
067s_O19


title: kidney cell 3183, Obese, 6 weeks

description:
kidney cell 3183
067s_O11


title: kidney cell 3187, Obese, 6 weeks

description:
kidney cell 3187
067s_O17


title: kidney cell 3182, Obese, 6 weeks

description:
kidney cell 3182
067s_O10


title: kidney cell 3178, Obese, 6 weeks

description:
kidney cell 3178
067s_N6


title: kidney cell 3179, Obese, 6 weeks

description:
kidney cell 3179
067s_N8


title: kidney cell 3180, Obese, 6 weeks

description:
kidney cell 3180
067s_N9


title: kidney cell 3181, Obese, 6 weeks

description:
kidney cell 3181
067s_O1


title: kidney cell 3177, Obese, 6 weeks

description:
kidney cell 3177
067s_N5


title: kidney cell 3174, Obese, 6 weeks

description:
kidney cell 3174
067s_N24


title: kidney cell 3175, Obese, 6 weeks

description:
kidney cell 3175
067s_N3


title: kidney cell 3200, Obese, 6 weeks

description:
kidney cell 3200
067s_O9


title: kidney cell 3176, Obese, 6 weeks

description:
kidney cell 3176
067s_N4


title: kidney cell 3172, Obese, 6 weeks

description:
kidney cell 3172
067s_N22


title: kidney cell 3169, Obese, 6 weeks

description:
kidney cell 3169
067s_N2


title: kidney cell 3167, Obese, 6 weeks

description:
kidney cell 3167
067s_N18


title: kidney cell 3170, Obese, 6 weeks

description:
kidney cell 3170
067s_N20


title: kidney cell 3171, Obese, 6 weeks

description:
kidney cell 3171
067s_N21


title: kidney cell 3166, Obese, 6 weeks

description:
kidney cell 3166
067s_N17


title: kidney cell 3188, Obese, 6 weeks

description:
kidney cell 3188
067s_O18


title: kidney cell 3164, Obese, 6 weeks

description:
kidney cell 3164
067s_N15


title: kidney cell 3162, Obese, 6 weeks

description:
kidney cell 3162
067s_N12


title: kidney cell 3163, Obese, 6 weeks

description:
kidney cell 3163
067s_N14


title: kidney cell 3161, Obese, 6 weeks

description:
kidney cell 3161
067s_N11


title: kidney cell 3165, Obese, 6 weeks

description:
kidney cell 3165
067s_N16


title: kidney cell 3158, Obese, 6 weeks

description:
kidney cell 3158
067s_M9


title: kidney cell 3160, Obese, 6 weeks

description:
kidney cell 3160
067s_N10


title: kidney cell 3159, Obese, 6 weeks

description:
kidney cell 3159
067s_N1


title: kidney cell 3157, Obese, 6 weeks

description:
kidney cell 3157
067s_M8


title: kidney cell 3154, Obese, 6 weeks

description:
kidney cell 3154
067s_M5


title: kidney cell 3156, Obese, 6 weeks

description:
kidney cell 3156
067s_M7


title: kidney cell 3153, Obese, 6 weeks

description:
kidney cell 3153
067s_M4


title: kidney cell 3151, Obese, 6 weeks

description:
kidney cell 3151
067s_M24


title: kidney cell 3173, Obese, 6 weeks

description:
kidney cell 3173
067s_N23


title: kidney cell 3150, Obese, 6 weeks

description:
kidney cell 3150
067s_M23


title: kidney cell 3152, Obese, 6 weeks

description:
kidney cell 3152
067s_M3


title: kidney cell 3149, Obese, 6 weeks

description:
kidney cell 3149
067s_M22


title: kidney cell 3168, Obese, 6 weeks

description:
kidney cell 3168
067s_N19


title: kidney cell 3147, Obese, 6 weeks

description:
kidney cell 3147
067s_M20


title: kidney cell 3146, Obese, 6 weeks

description:
kidney cell 3146
067s_M2


title: kidney cell 3148, Obese, 6 weeks

description:
kidney cell 3148
067s_M21


title: kidney cell 3145, Obese, 6 weeks

description:
kidney cell 3145
067s_M19


title: kidney cell 3144, Obese, 6 weeks

description:
kidney cell 3144
067s_M18


title: kidney cell 3143, Obese, 6 weeks

description:
kidney cell 3143
067s_M17


title: kidney cell 3141, Obese, 6 weeks

description:
kidney cell 3141
067s_M15


title: kidney cell 3138, Obese, 6 weeks

description:
kidney cell 3138
067s_M11


title: kidney cell 3142, Obese, 6 weeks

description:
kidney cell 3142
067s_M16


title: kidney cell 3155, Obese, 6 weeks

description:
kidney cell 3155
067s_M6


title: kidney cell 3136, Obese, 6 weeks

description:
kidney cell 3136
067s_M1


title: kidney cell 3137, Obese, 6 weeks

description:
kidney cell 3137
067s_M10


title: kidney cell 3135, Obese, 6 weeks

description:
kidney cell 3135
067s_L9


title: kidney cell 3134, Obese, 6 weeks

description:
kidney cell 3134
067s_L8


title: kidney cell 3139, Obese, 6 weeks

description:
kidney cell 3139
067s_M12


title: kidney cell 3133, Obese, 6 weeks

description:
kidney cell 3133
067s_L7


title: kidney cell 3131, Obese, 6 weeks

description:
kidney cell 3131
067s_L5


title: kidney cell 3132, Obese, 6 weeks

description:
kidney cell 3132
067s_L6


title: kidney cell 3128, Obese, 6 weeks

description:
kidney cell 3128
067s_L24


title: kidney cell 3130, Obese, 6 weeks

description:
kidney cell 3130
067s_L4


title: kidney cell 3126, Obese, 6 weeks

description:
kidney cell 3126
067s_L22


title: kidney cell 3124, Obese, 6 weeks

description:
kidney cell 3124
067s_L20


title: kidney cell 3119, Obese, 6 weeks

description:
kidney cell 3119
067s_L14


title: kidney cell 3127, Obese, 6 weeks

description:
kidney cell 3127
067s_L23


title: kidney cell 3123, Obese, 6 weeks

description:
kidney cell 3123
067s_L2


title: kidney cell 3120, Obese, 6 weeks

description:
kidney cell 3120
067s_L16


title: kidney cell 3122, Obese, 6 weeks

description:
kidney cell 3122
067s_L19


title: kidney cell 3118, Obese, 6 weeks

description:
kidney cell 3118
067s_L12


title: kidney cell 3116, Obese, 6 weeks

description:
kidney cell 3116
067s_L10


title: kidney cell 3117, Obese, 6 weeks

description:
kidney cell 3117
067s_L11


title: kidney cell 3115, Obese, 6 weeks

description:
kidney cell 3115
067s_L1


title: kidney cell 3140, Obese, 6 weeks

description:
kidney cell 3140
067s_M14


title: kidney cell 3114, Obese, 6 weeks

description:
kidney cell 3114
067s_K9


title: kidney cell 3113, Obese, 6 weeks

description:
kidney cell 3113
067s_K8


title: kidney cell 3110, Obese, 6 weeks

description:
kidney cell 3110
067s_K5


title: kidney cell 3111, Obese, 6 weeks

description:
kidney cell 3111
067s_K6


title: kidney cell 3112, Obese, 6 weeks

description:
kidney cell 3112
067s_K7


title: kidney cell 3108, Obese, 6 weeks

description:
kidney cell 3108
067s_K3


title: kidney cell 3106, Obese, 6 weeks

description:
kidney cell 3106
067s_K23


title: kidney cell 3107, Obese, 6 weeks

description:
kidney cell 3107
067s_K24


title: kidney cell 3102, Obese, 6 weeks

description:
kidney cell 3102
067s_K2


title: kidney cell 3121, Obese, 6 weeks

description:
kidney cell 3121
067s_L17


title: kidney cell 3103, Obese, 6 weeks

description:
kidney cell 3103
067s_K20


title: kidney cell 3105, Obese, 6 weeks

description:
kidney cell 3105
067s_K22


title: kidney cell 3125, Obese, 6 weeks

description:
kidney cell 3125
067s_L21


title: kidney cell 3129, Obese, 6 weeks

description:
kidney cell 3129
067s_L3


title: kidney cell 3099, Obese, 6 weeks

description:
kidney cell 3099
067s_K17


title: kidney cell 3098, Obese, 6 weeks

description:
kidney cell 3098
067s_K16


title: kidney cell 3100, Obese, 6 weeks

description:
kidney cell 3100
067s_K18


title: kidney cell 3095, Obese, 6 weeks

description:
kidney cell 3095
067s_K12


title: kidney cell 3094, Obese, 6 weeks

description:
kidney cell 3094
067s_K11


title: kidney cell 3093, Obese, 6 weeks

description:
kidney cell 3093
067s_K10


title: kidney cell 3097, Obese, 6 weeks

description:
kidney cell 3097
067s_K15


title: kidney cell 3096, Obese, 6 weeks

description:
kidney cell 3096
067s_K14


title: kidney cell 3091, Obese, 6 weeks

description:
kidney cell 3091
067s_J9


title: kidney cell 3092, Obese, 6 weeks

description:
kidney cell 3092
067s_K1


title: kidney cell 3090, Obese, 6 weeks

description:
kidney cell 3090
067s_J8


title: kidney cell 3089, Obese, 6 weeks

description:
kidney cell 3089
067s_J6


title: kidney cell 3109, Obese, 6 weeks

description:
kidney cell 3109
067s_K4


title: kidney cell 3104, Obese, 6 weeks

description:
kidney cell 3104
067s_K21


title: kidney cell 3088, Obese, 6 weeks

description:
kidney cell 3088
067s_J5


title: kidney cell 3085, Obese, 6 weeks

description:
kidney cell 3085
067s_J24


title: kidney cell 3101, Obese, 6 weeks

description:
kidney cell 3101
067s_K19


title: kidney cell 3084, Obese, 6 weeks

description:
kidney cell 3084
067s_J23


title: kidney cell 3083, Obese, 6 weeks

description:
kidney cell 3083
067s_J22


title: kidney cell 3079, Obese, 6 weeks

description:
kidney cell 3079
067s_J18


title: kidney cell 3080, Obese, 6 weeks

description:
kidney cell 3080
067s_J2


title: kidney cell 3082, Obese, 6 weeks

description:
kidney cell 3082
067s_J21


title: kidney cell 3077, Obese, 6 weeks

description:
kidney cell 3077
067s_J16


title: kidney cell 3074, Obese, 6 weeks

description:
kidney cell 3074
067s_J12


title: kidney cell 3075, Obese, 6 weeks

description:
kidney cell 3075
067s_J14


title: kidney cell 3081, Obese, 6 weeks

description:
kidney cell 3081
067s_J20


title: kidney cell 3076, Obese, 6 weeks

description:
kidney cell 3076
067s_J15


title: kidney cell 3073, Obese, 6 weeks

description:
kidney cell 3073
067s_J11


title: kidney cell 3078, Obese, 6 weeks

description:
kidney cell 3078
067s_J17


title: kidney cell 3072, Obese, 6 weeks

description:
kidney cell 3072
067s_J10


title: kidney cell 3071, Obese, 6 weeks

description:
kidney cell 3071
067s_J1


title: kidney cell 3070, Obese, 6 weeks

description:
kidney cell 3070
067s_I9


title: kidney cell 3068, Obese, 6 weeks

description:
kidney cell 3068
067s_I7


title: kidney cell 3067, Obese, 6 weeks

description:
kidney cell 3067
067s_I5


title: kidney cell 3087, Obese, 6 weeks

description:
kidney cell 3087
067s_J4


title: kidney cell 3066, Obese, 6 weeks

description:
kidney cell 3066
067s_I4


title: kidney cell 3064, Obese, 6 weeks

description:
kidney cell 3064
067s_I24


title: kidney cell 3086, Obese, 6 weeks

description:
kidney cell 3086
067s_J3


title: kidney cell 3065, Obese, 6 weeks

description:
kidney cell 3065
067s_I3


title: kidney cell 3063, Obese, 6 weeks

description:
kidney cell 3063
067s_I23


title: kidney cell 3062, Obese, 6 weeks

description:
kidney cell 3062
067s_I22


title: kidney cell 3061, Obese, 6 weeks

description:
kidney cell 3061
067s_I21


title: kidney cell 3060, Obese, 6 weeks

description:
kidney cell 3060
067s_I20


title: kidney cell 3059, Obese, 6 weeks

description:
kidney cell 3059
067s_I2


title: kidney cell 3057, Obese, 6 weeks

description:
kidney cell 3057
067s_I18


title: kidney cell 3058, Obese, 6 weeks

description:
kidney cell 3058
067s_I19


title: kidney cell 3056, Obese, 6 weeks

description:
kidney cell 3056
067s_I16


title: kidney cell 3053, Obese, 6 weeks

description:
kidney cell 3053
067s_I12


title: kidney cell 3055, Obese, 6 weeks

description:
kidney cell 3055
067s_I15


title: kidney cell 3051, Obese, 6 weeks

description:
kidney cell 3051
067s_I10


title: kidney cell 3052, Obese, 6 weeks

description:
kidney cell 3052
067s_I11


title: kidney cell 3054, Obese, 6 weeks

description:
kidney cell 3054
067s_I14


title: kidney cell 3069, Obese, 6 weeks

description:
kidney cell 3069
067s_I8


title: kidney cell 3050, Obese, 6 weeks

description:
kidney cell 3050
067s_I1


title: kidney cell 3049, Obese, 6 weeks

description:
kidney cell 3049
067s_H9


title: kidney cell 3044, Obese, 6 weeks

description:
kidney cell 3044
067s_H4


title: kidney cell 3045, Obese, 6 weeks

description:
kidney cell 3045
067s_H5


title: kidney cell 3042, Obese, 6 weeks

description:
kidney cell 3042
067s_H23


title: kidney cell 3041, Obese, 6 weeks

description:
kidney cell 3041
067s_H22


title: kidney cell 3043, Obese, 6 weeks

description:
kidney cell 3043
067s_H3


title: kidney cell 3038, Obese, 6 weeks

description:
kidney cell 3038
067s_H2


title: kidney cell 3040, Obese, 6 weeks

description:
kidney cell 3040
067s_H21


title: kidney cell 3039, Obese, 6 weeks

description:
kidney cell 3039
067s_H20


title: kidney cell 3037, Obese, 6 weeks

description:
kidney cell 3037
067s_H19


title: kidney cell 3036, Obese, 6 weeks

description:
kidney cell 3036
067s_H18


title: kidney cell 3035, Obese, 6 weeks

description:
kidney cell 3035
067s_H17